- Prometheus occurs in the years 2089 – 2093, landing on LV-223
- David escapes LV-223 and creates the Xenomorphs between 2093 and 2104
- Covenant occurs in the year 2104
- Presumably, sometime between 2093 and 2122 the infected space jockey crashes on LV-426
- Nostromo lands on LV-426 in the year 2122 in the original Alien movie.
The black goo:
The xenomorphs were created as the result of the Engineer's morphic goo -- but not by the engineers. The goo promotes a sort of hyper-evolution within any organism it comes into contact with.
In the beginning of Prometheus we see the goo used as a means for promoting life - where an engineer eats the goo and, with his sacrificial self, seeds life on... our primordial Earth.
The xenomorph is a weaponized version of an infected species - built using the infected species' own DNA; but whether that weaponized result was intended by the originating engineers, or not, is not disclosed.
LV-223 / Prometheus:
Humans, looking for their Creators (the engineers), arrive aboard Prometheus on LV-223.
The engineers on LV-223 are all dead except for one who is in stasis. Evidently they had a sort of civil war or techo-disaster concurrent with some of them making idols of and worshiping... someone who looks like themselves. There's a hologram that shows some engineers running from something; but it's a mystery what they were running from in the hologram.
David the Android:
Accompanying the humans in Prometheus is a self-worshiping android named David -- and he makes things worse - for everybody.
It is David who, along with Dr. Shaw, escapes from LV-223 to an unnamed planet inhabited by humanoids having an appearance similar to the engineers. It is also David who, upon arrival on the unnamed planet, releases the black goo and genocides the humanoid engineeresque inhabitants.
David created the Xenomorphs:
David, while marooned alone on the unnamed planet, "creates" the xenomorphs after studying and using the goo to manifest his own insane vision -- culminating with the familiar eggs and face-huggers.
The Covenant is a colony ship that is lured into going off course to investigate a radio signal of someone singing John's Denver's "country road" emanating from David's unnamed, unknown, uncharted planet.
The first human host seeded by David's face-hugger is the faithful captain of the Covenant.